Interpretive Summary: Diseases caused by phytoplasmas are responsible for economic losses in hundreds of crop plant species worldwide, and many are quarantine concerns to the U.S., because their introduction would reduce farm profitability and threaten the agricultural export economy. There is pressing need for effective disease control strategies; analyses of phytoplasma genomes present opportunities to address this deficiency. In this chapter, we present original data and analyses of four completely sequenced phytoplasma genomes. The results elucidate genome evolution that resulted in phytoplasma species that became adapted to a vastly broad range of plant host-insect vector ecosystems worldwide, in a process that undoubtedly gave rise to many more species than currently known. Our findings encourage anticipation that unexpected, perhaps surprising, phytoplasma diversity will be uncovered through continued genomic research. Yet, we show that a common genomic thread unites all phytoplasmas. All contain phage-based genomic islands (sequence variable mosaics). Through integration of phage genomes into the phytoplasma progenitor chromosome, new capabilities were acquired for transkingdom parasitism in plants and insects, while genes became lost when no longer needed for synthesis of nutrients that could be imported from hosts. Additional genes were acquired from other organisms through targeted insertion of mobile gene cassette-like elements into the phage-based islands. The findings make it apparent that evolutionary emergence of phytoplasmas is largely attributable to a singularly critical event, genome fusion. Students of parasitism and pathogenicity; scientists interested in molecular markers of pathogen lineages; scientists interested in genome features determining the physiology of bacterium-host interactions; diagnostics companies and quarantine agencies; and companies, government agencies, and universities involved in work aimed at disease control, will be interested in the analyses and insights.

Technical Abstract:
Phytoplasmas possess the smallest genomes known among plant pathogens. Yet, these biotrophic microbes exist as obligate parasites and pathogens of both plants and insects. After their evolutionary divergence from an acholeplasmalike ancestor and emergence as a discrete clade, phytoplasmas evolved to give rise to widely divergent lineages. To learn genomic features shared by phytoplasmas and other cell-wall-less bacteria, and features that are unique to phytoplasmas, we did comparative analyses of four completely sequenced phytoplasma genomes, partial genomes of other phytoplasmas, the genome of ancestral relative Acholeplasma laidlawii, and the genome of Mycoplasma genitalium, a model wall-less bacterium thought to have the minimum gene complement among cultivable cellular organisms. Global synteny, found only between related phytoplasmas within a species, was interrupted by genomic islands (sequence variable mosaics, SVMs) formed through repeated and targeted insertion of phage genomes into the chromosomes. Regions of microsynteny across species reflected evolutionarily conserved and coordinately regulated genes. Hypervariable regions within the phage genomes were sites of targeted insertion of foreign genes by mechanisms resembling integron/mobile gene cassette systems. The analyses identified genes unique to phytoplasmas, many of which were located in SVMs, and supported the hypothesis that SVM formation triggered evolution of the phytoplasma clade. The data indicated that inability of phytoplasmas to grow in axenic culture could be attributed, in part, to identifiable genomic features related to gene loss during ongoing evolutionary adaptation to obligate parasitism, and the findings pointed to niche adaptations encoded by phytoplasma genomes, as well as potential virulence factors.